LAMMPS (4 Nov 2022)
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain

units real

boundary p p p

atom_style full

pair_style lj/class2/coul/cut 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

variable T equal 530

read_data trimer.data   extra/bond/per/atom 5   extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (-200 -200 -200) to (200 200 200)
  1 by 2 by 2 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  48 atoms
  scanning bonds ...
  8 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  33 = max dihedrals/atom
  scanning impropers ...
  26 = max impropers/atom
  reading bonds ...
  50 bonds
  reading angles ...
  84 angles
  reading dihedrals ...
  127 dihedrals
  reading impropers ...
  20 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     8 = max # of 1-3 neighbors
    17 = max # of 1-4 neighbors
    46 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.007 seconds

molecule mol1 grow_styrene_pre.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  30 atoms with max type 4
  31 bonds with max type 6
  51 angles with max type 10
  73 dihedrals with max type 13
  13 impropers with max type 3
molecule mol2 grow_styrene_post.molecule_template
Read molecule template mol2:
  1 molecules
  1 fragments
  46 atoms with max type 4
  48 bonds with max type 6
  81 angles with max type 10
  121 dihedrals with max type 13
  19 impropers with max type 3

fix myrxns all bond/react stabilization yes statted_grp .03     react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map         modify_create fit create_fit overlap 2.0         stabilize_steps 200 max_rxn 30
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100

fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1

thermo_style custom step temp press density f_myrxns[1]

thermo 100

dump 1 all xyz 1 test_vis.xyz

run 8000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 6 of 6 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 77 77 77
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 35.37 | 35.56 | 36.15 Mbytes
   Step          Temp          Press         Density      f_myrxns[1]  
         0   0              0.076588866    8.1070333e-06  0            
       100   598.29879     -0.17888669     1.0809378e-05  1            
       200   699.08337      0.11172183     1.0809378e-05  1            
       300   931.85797     -0.13923465     1.3511722e-05  2            
       400   893.78126      0.14680427     1.3511722e-05  2            
       500   1001.0848     -0.021703999    1.6214067e-05  3            
       600   989.24943      0.04641672     1.6214067e-05  3            
       700   1244.794      -0.19464667     1.8916411e-05  4            
       800   1210.997      -0.06710628     1.8916411e-05  4            
       900   1310.0005      0.099408095    2.1618755e-05  5            
      1000   1640.5956     -0.05975911     2.1618755e-05  5            
      1100   1380.7273     -0.025206389    2.1618755e-05  5            
      1200   1637.6542      0.057149266    2.43211e-05    6            
      1300   1757.3409      0.3232123      2.43211e-05    6            
      1400   1664.5048     -0.29656858     2.7023444e-05  7            
      1500   1578.9691      0.21997047     2.7023444e-05  7            
      1600   1848.9227     -0.11783672     2.9725789e-05  8            
      1700   1981.1695      0.28374154     2.9725789e-05  8            
      1800   2330.8852     -0.082109894    3.2428133e-05  9            
      1900   2177.4096      0.23853778     3.2428133e-05  9            
      2000   2095.1618     -1.5405667      3.5130478e-05  10           
      2100   2272.2653      0.05572226     3.5130478e-05  10           
      2200   2599.5994     -2.2307507      3.7832822e-05  11           
      2300   2457.7904      0.40228312     3.7832822e-05  11           
      2400   2372.9736     -3.3415973      4.0535167e-05  12           
      2500   2427.4613     -0.16211888     4.0535167e-05  12           
      2600   3022.2608     -4.3278098      4.3237511e-05  13           
      2700   3115.6526      0.013828954    4.3237511e-05  13           
      2800   2841.7091     -6.4163443      4.5939855e-05  14           
      2900   3047.8436      0.16052429     4.5939855e-05  14           
      3000   3373.7997     -7.7904706      4.86422e-05    15           
      3100   3381.6653      0.35152687     4.86422e-05    15           
      3200   3589.5561     -10.754027      5.1344544e-05  16           
      3300   3473.4415     -0.13274479     5.1344544e-05  16           
      3400   3696.3283     -13.75504       5.4046889e-05  17           
      3500   3486.5442     -0.31091832     5.4046889e-05  17           
      3600   3647.0818      0.34662993     5.4046889e-05  17           
      3700   3636.7138     -0.041981737    5.4046889e-05  17           
      3800   3427.6532      0.42008936     5.6749233e-05  18           
      3900   3574.0094     -0.05475272     5.6749233e-05  18           
      4000   4158.9339      0.14426361     5.9451578e-05  19           
      4100   3862.5026      0.094232438    5.9451578e-05  19           
      4200   3969.4378     -0.10602108     6.2153922e-05  20           
      4300   3840.0126      0.29190336     6.2153922e-05  20           
      4400   4365.9912     -36.954812      6.4856266e-05  21           
      4500   4565.3708      0.061879092    6.4856266e-05  21           
      4600   4565.491      -70.588435      6.7558611e-05  22           
      4700   4570.2702     -0.56661378     6.7558611e-05  22           
      4800   4445.786       0.20534323     6.7558611e-05  22           
      4900   4782.6436      0.012783481    7.0260955e-05  23           
      5000   4777.2132      0.092416308    7.0260955e-05  23           
      5100   4944.0402      0.11614993     7.29633e-05    24           
      5200   5139.165      -0.23180938     7.29633e-05    24           
      5300   4647.2328      0.13570142     7.5665644e-05  25           
      5400   4982.7355     -0.25477884     7.5665644e-05  25           
      5500   5400.5924      0.19902824     7.8367989e-05  26           
      5600   5761.3552      0.083102065    7.8367989e-05  26           
      5700   5723.8581      0.039332796    8.1070333e-05  27           
      5800   5548.0789     -0.14511631     8.1070333e-05  27           
      5900   5358.5431     -0.099694264    8.3772677e-05  28           
      6000   5591.2678      9.9924655e-05  8.3772677e-05  28           
      6100   6101.8008      0.26538732     8.6475022e-05  29           
      6200   5848.9979      0.091137862    8.6475022e-05  29           
      6300   5582.1828     -0.039900602    8.9177366e-05  30           
      6400   6077.0548      0.3191104      8.9177366e-05  30           
      6500   5794.6827      0.69322336     8.9177366e-05  30           
      6600   5610.4331      0.080420058    8.9177366e-05  30           
      6700   5615.3492      0.12810868     8.9177366e-05  30           
      6800   5900.9749     -0.31704866     8.9177366e-05  30           
      6900   6233.9524      0.010288514    8.9177366e-05  30           
      7000   5972.7488     -1.0442089      8.9177366e-05  30           
      7100   6258.1332      0.56270399     8.9177366e-05  30           
      7200   6172.5919     -0.19595153     8.9177366e-05  30           
      7300   5898.7547      0.020862491    8.9177366e-05  30           
      7400   5815.1659     -0.0020680171   8.9177366e-05  30           
      7500   6003.867      -0.12288131     8.9177366e-05  30           
      7600   5966.0609     -0.1504333      8.9177366e-05  30           
      7700   6274.3331     -0.62752757     8.9177366e-05  30           
      7800   6051.0914      0.22821201     8.9177366e-05  30           
      7900   5981.5209     -0.19623554     8.9177366e-05  30           
      8000   5835.4657      0.3602475      8.9177366e-05  30           
Loop time of 13.936 on 4 procs for 8000 steps with 528 atoms

Performance: 49.598 ns/day, 0.484 hours/ns, 574.051 timesteps/s, 303.099 katom-step/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.001058   | 0.78388    | 3.1317     | 153.1 |  5.62
Bond    | 0.0031874  | 2.0525     | 8.1984     | 247.7 | 14.73
Neigh   | 0.53495    | 0.53527    | 0.53551    |   0.0 |  3.84
Comm    | 0.01177    | 0.012451   | 0.013306   |   0.5 |  0.09
Output  | 1.3336     | 1.4735     | 1.7322     |  13.2 | 10.57
Modify  | 0.55142    | 9.0568     | 12.031     | 163.3 | 64.99
Other   |            | 0.02159    |            |       |  0.15

Nlocal:            132 ave         528 max           0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost:              0 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:        9115.75 ave       36463 max           0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

Total # of neighbors = 36463
Ave neighs/atom = 69.058712
Ave special neighs/atom = 11.409091
Neighbor list builds = 771
Dangerous builds = 0

# write_data final.data nofix
Total wall time: 0:00:13
